Table 3.
Locusa | CNV type | CNV frequency
|
Beta b | P value c | Genes | ||
---|---|---|---|---|---|---|---|
Cases | Controls | ||||||
Chr5: 68,921,426-70,412,247 | Copy number/dosagee | Duplication | 43 (4.97%) | 16 (1.59%) | 0.69 | 3.37 × 10−4 | SMA4, SERF1, SERF1B, SMN2, SMA3, NAIP, GTF2H2, GTF2H2D, OCLN d |
Deletion | 22 (2.54%) | 36 (3.57%) | |||||
Non-missing | 865 (100%) | 1008 (100%) | |||||
| |||||||
chr6:79,034,386-79,090,197 | Duplication | Duplication | 83 (8.99%) | 38 (3.49%) | 1.05 | 1.04 × 10−6 | Gene desert |
Deletion | 448 (48.54%) | 542 (49.77%) | |||||
Non-missing | 923 (100%) | 1089 (100%) |
The starting and the ending point are defined by the probes whose P values have a clear deviation from the rest.
The P value and beta of this region is annotated by the most significant probe in this CNV.
OCLN is located less than 30 kb downstream of this region.
This CNV was analyzed as ≤1= deletion, 2=normal diploid, ≥3=duplication. For cases: Deletions: 4/22 had a dosage score of 0.667 (18/22 had a score of 1, or heterozygous for deletion); Duplications: 39/43 had a dosage score of 3 (heterozygous) and the remainder had a mean score of 3.3. For controls: Deletions: 11/36 had a dosage score of 0.667, remainder scoring 1; Duplications: 13/22 had a dosage score of 3, 2/22 had a score of 3.3 and 1/22 had a score of 4 (homozygous duplication).